Scunthorpe,were desperately unlucky to play for 80 minutes with 10 men.
Cliff Byrne was sent off in the opening minutes when the referee ruled he had fouled Jeremie Aliadiere. The penalty was a harsh decision but, having awarded it, the referee had no alternative but to dismiss Byrne as the last man.
Adam Johnson, an England U21 international, made no mistake from the spot to record his tenth goal of the season.
After that the outcome of the game was never in doubt. Middlesbrough dominated the first half and should have piled on the goals, with Johnson striking a post and Tony McMahon flashing a shot wide.
Scunthorpe were putting up a dogged defensive display but a second goal was almost inevitable and Rhys Williams provided it with a well-drilled left-foot shot from the edge of the penalty area.
Aliadiere marked his return to the side with a goal a moment after the restart.
Danny Coyne, recalled in goal by Middlesbrough, saved from Grant McCann as the visitors attempted to reduce the arrears.
There was a shock development for Boro fans in the closing minute though. A linesman had spotted an offence by striker Leroy Lita in the penalty area. He brought it to the attention of the referee who then flashed a red card.